Stone monuments in archaeological contexts are particularly vulnerable to biodeterioration due to environmental exposure and the intrinsic properties of their materials. Biodeterioration occurs through the action of microorganisms and macroscopic organisms, whose effects are influenced by factors such as stone material type and environmental conditions. Traditional approaches to managing biological growth often relied on chemical biocides but increasing environmental and regulatory concerns have led to a shift towards sustainable alternatives. Recent research has emphasized eco-friendly solutions, investigating essential oils (EOs) along with engineered mesoporous silica nanoparticles (MSNs) and halloysite nanotubes (HNTs) as effective carriers to enhance the stability and efficacy of natural biocides. This contribution addresses the critical challenge of managing biodeterioration on stone monuments exposed to external environments, emphasizing the necessity of a multidisciplinary approach. Indeed, synergistic methods that integrate indirect treatments, environmental monitoring, and selective use of biocides are critical for reducing environmental impact while preserving material integrity. Ongoing research aims to refine sustainable biocidal formulations and application methods, exploring hybrid models that combine biological, chemical, and physical interventions. By fostering such integrated conservation strategies, the field can balance heritage preservation with environmental sustainability, ensuring the longevity of outdoor stone artifacts.